There's no reason (that I can think of) that an SI engine and transmission would not fit. Pretty short engines height-wise, if I recall the last one we had in the shop, the engine was canted for clearance anyway.
The S2000 drivetrain is a different story. You could probably use the engine in a transverse configuration (as with the Civic), but as the S2000 is rear wheel drive with a longitundinal layout, the combination will not fit in a spyder.
There are several people with assorted in-line four cylinder engines in their spyders, but I believe they are all mounted transversely (like a Civic). The length of the car between the axle centerline and the firewall dictates the overall length of your engine/transmission package. An in-line four cylinder is substantially longer than a flat four. Most in-line four cylinders are longer than the flat six in our car. A rotary engine is very short and fits quite nicely.
The subaru engine mated to the subaru 2wd transmission may be closest to what you are looking for. But there is no reason that a compact FWD drivetrain couldn't be used (honda or acura). How about an Acura RSX drivetrain?
angela